autogrid - preparing protein and ligand for AutoDock analysis
autogrid4 [
options] -p gridparameterfile
AutoGrid prepares a 3D grid representation of the non-covalent
interaction energies that various user-specified ligand atom types will
experience around a user-specified target macromolecule. In addition, the
electrostatic potential and desolvation free energy grid maps may also be
calculated. The grid maps are stored in plain text files with the extension
'.map' and are required by AutoDock 4 to perform dockings. AutoGrid also
outputs a '.xyz' file which describes the spatial extents of the grid box, and
an AVS field '.fld' file which describes the consistent set of atomic affinity
grid maps that were calculated together for a given target macromolecule.
Note: it is necessary to compute grid maps for all the atom types in the
ligand or set of ligands that will be docked, as well as an electrostatic
potential grid map and a desolvation free energy map. For example, if a ligand
has an aliphatic carbon and a hydrogen-bond-accepting oxygen atom, it would be
necessary to compute both a 'C' map and an 'OA' map. See
http://autodock.scripps.edu/faqs-help/faq/where-do-i-set-the-autodock-4-force-field-parameters
for more information about AutoDock 4 atom types.
The input to AutoGrid is best prepared with the program suite AutoDockTools.
There is no way to run autodock4 without a grid.
-o Use old PDBq format (q in columns 55-61)
- -u
- Usage information, also -h on Debian.
- -d
- Increased verbosity of messages to help debugging.
- -l
- logfile
- -p
- filename Specifies Grid Parameter File
A range of tests is made available with the AutoGrid sources that can be used as
follows:
$ D=/usr/share/doc/autogrid/Tests
$ cd /tmp
$ ln -s $D/AD4_parameters.dat .
$ gunzip -c $D/hsg1_sm.pdbqt.gz > hsg1_sm.pdbqt
$ autogrid4 -p $D/hsg1_no_receptor_types.gpf -l hsg1_no_receptor_types.glg
- This command prepares grid map files for each of the
AutoDock atom types specified in the grid parameter file (in this case:
hsg1_sm.A.map, hsg1_sm.C.map, hsg1_sm.d.map, hsg1_sm.e.map, hsg1_sm.HD.map,
hsg1_sm.NA.map, hsg1_sm.N.map, hsg1_sm.OA.map), the AVS field file
(hsg1_sm.maps.fld) and hsg1_sm.maps.xyz. To perform the cocking calculation,
AutoDock should be executed, though it demands a separate docking parameter
file (with extension .dpf). The 'DPF' refers to the grid map files that are
necessary to the docking and allows the setting of other important
parameters, such as the search method and how many dockings to perform.
-
autodock(1),
runAdt(1).
http://autodock.scripps.edu
This software is made available under the terms of the GNU Public License
version 2 or later. This implies that this software may be redistributed if
the source is made available. It would however help the future development of
the AutoDockSuite if you register yourself at
http://autodock.scripps.edu/downloads.
The most prominent author of the version 4 of AutoDock is G. Morris
<
[email protected]>. See the AUTHORS file in /usr/share/doc/autogrid
for details.
This manual page was written by Steffen Moeller <
[email protected]> and
much revised by upstream author Garrett Morris. It was prepared for the Debian
project but may be used by others and is hopefully adopted by the upstream
developers.